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2.12

Template

- Add a Github Action Workflow to the pipeline template that tests a successful download with `nf-core download` ([2618](https://github.com/nf-core/tools/pull/2618))
- Use `pre-commit` to lint files in GitHub CI ([2635](https://github.com/nf-core/tools/pull/2635))
- Use pdiff also on gitpod for nf-test ([2640](https://github.com/nf-core/tools/pull/2640))
- switch to new image syntax in readme ([2645](https://github.com/nf-core/tools/pull/2645))
- Add conda channel order to nextflow.config ([2094](https://github.com/nf-core/tools/pull/2094))
- Fix tyop in pipeline nextflow.config ([2664](https://github.com/nf-core/tools/pull/2664))
- Remove `nfcore_external_java_deps.jar` from lib directory in pipeline template ([2675](https://github.com/nf-core/tools/pull/2675))
- Add function to check `-profile` is well formatted ([2678](https://github.com/nf-core/tools/pull/2678))
- Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message ([2680](https://github.com/nf-core/tools/pull/2680))
- add 👀👍🏻🎉😕 reactions to fix-linting-bot action ([2692](https://github.com/nf-core/tools/pull/2692))

Linting

- Fix linting of a pipeline with patched custom module ([2669](https://github.com/nf-core/tools/pull/2669))
- linting a pipeline also lints the installed subworkflows ([2677](https://github.com/nf-core/tools/pull/2677))
- environment.yml name must be lowercase ([2676](https://github.com/nf-core/tools/pull/2676))
- allow ignoring specific files when template_strings ([2686](https://github.com/nf-core/tools/pull/2686))
- lint `nextflow.config` default values match the ones specified in `nextflow_schema.json` ([2684](https://github.com/nf-core/tools/pull/2684))

Modules

- Fix empty json output for `nf-core list local` ([2668](https://github.com/nf-core/tools/pull/2668))

General

- Run CI-pytests for nf-core tools on self-hosted runners ([2550](https://github.com/nf-core/tools/pull/2550))
- Add Ruff linter and formatter replacing Black, isort and pyupgrade ([2620](https://github.com/nf-core/tools/pull/2620))
- Set pdiff as nf-test differ in Docker image for Gitpod ([2642](https://github.com/nf-core/tools/pull/2642))
- Fix Renovate Dockerfile updating issues ([2648](https://github.com/nf-core/tools/pull/2648) and [#2651](https://github.com/nf-core/tools/pull/2651))
- Add new subcommand `nf-core tui`, which launches a TUI (terminal user interface) to intuitively explore the command line flags, built using [Trogon](https://github.com/Textualize/trogon) ([#2655](https://github.com/nf-core/tools/pull/2655))
- Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([2662](https://github.com/nf-core/tools/pull/2662))
- Handle api redirects from the old site ([2672](https://github.com/nf-core/tools/pull/2672))
- Remove redundanct v in pipeline version for emails ([2667](https://github.com/nf-core/tools/pull/2667))
- add function to check `-profile` is well formatted ([2678](https://github.com/nf-core/tools/pull/2678))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.14 ([2674](https://github.com/nf-core/tools/pull/2674))
- Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([2630](https://github.com/nf-core/tools/pull/2630))
- Update mshick/add-pr-comment action to v2 ([2632](https://github.com/nf-core/tools/pull/2632))
- update python image version in docker file ([2636](https://github.com/nf-core/tools/pull/2636))
- Update actions/cache action to v4 ([2666](https://github.com/nf-core/tools/pull/2666))
- Update peter-evans/create-or-update-comment action to v4 ([2683](https://github.com/nf-core/tools/pull/2683))
- Update peter-evans/create-or-update-comment action to v4 ([2695](https://github.com/nf-core/tools/pull/2695))

2.11.1

Template

- Rename `release-announcments.yml` to `release-announcements.yml` ([2610](https://github.com/nf-core/tools/pull/2610))
- Fix `nextflow.config` `docker.runOptions` ([2607](https://github.com/nf-core/tools/pull/2607))

General

- Only dump `modules.json` when it is modified ([2609](https://github.com/nf-core/tools/pull/2609))

2.11

Template

- Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([2465](https://github.com/nf-core/tools/pull/2465))
- Fancier syntax highlighting for example samplesheets in the usage.md template ([2503](https://github.com/nf-core/tools/pull/2503))
- Use closure for multiqc ext.args ([2509](https://github.com/nf-core/tools/pull/2509))
- Fix how the modules template references the conda environment file ([2540](https://github.com/nf-core/tools/pull/2540))
- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([2569](https://github.com/nf-core/tools/pull/2569))
- Pin the version of nf-validation ([2579](https://github.com/nf-core/tools/pull/2579))
- Disable process selector warnings by default ([2161](https://github.com/nf-core/tools/issues/2161))
- Remove `docker.userEmulation` from nextflow.config in pipeline template ([2580](https://github.com/nf-core/tools/pull/2580))

Download

- Add `docker://` prefix for absolute container URIs as well ([2576](https://github.com/nf-core/tools/pull/2576)).
- Bugfix for AttributeError: `ContainerError` object has no attribute `absoluteURI` ([2543](https://github.com/nf-core/tools/pull/2543)).

Linting

- Fix incorrectly failing linting if 'modules' was not found in meta.yml ([2447](https://github.com/nf-core/tools/pull/2447))
- Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([2448](https://github.com/nf-core/tools/pull/2448))
- Add pyupgrade to pre-commit config and dev requirements as mentioned in [2200](https://github.com/nf-core/tools/issues/2200)
- Check for spaces in modules container URLs ([2452](https://github.com/nf-core/tools/issues/2452))
- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables when linting a pipeline. ([2507](https://github.com/nf-core/tools/pull/2507))
- Lint nf-test main.nf.test tags include all used components in chained tests ([2572](https://github.com/nf-core/tools/pull/2572))
- Don't fail linting if md5sum for empty files are found in a stub test ([2571](https://github.com/nf-core/tools/pull/2571))
- Check for existence of test profile ([2478](https://github.com/nf-core/tools/pull/2478))

Modules

- Added stub test creation to `create_test_yml` ([2476](https://github.com/nf-core/tools/pull/2476))
- Replace ModulePatch by ComponentPatch ([2482](https://github.com/nf-core/tools/pull/2482))
- Fixed `nf-core modules lint` to work with new module structure for nf-test ([2494](https://github.com/nf-core/tools/pull/2494))
- Add option `--migrate-pytest` to create a module with nf-test taking into account an existing module ([2549](https://github.com/nf-core/tools/pull/2549))
- When installing modules and subworkflows, automatically create the `./modules` directory if it doesn't exist ([2563](https://github.com/nf-core/tools/issues/2563))
- When `.nf-core.yml` is not found create it in the current directory instead of the root filesystem ([2237](https://github.com/nf-core/tools/issues/2237))
- Modules `--migrate-pytest` copies template scripts ([2568](https://github.com/nf-core/tools/pull/2568))

Subworkflows

- Added stub test creation to `create_test_yml` ([2476](https://github.com/nf-core/tools/pull/2476))
- Fixed `nf-core subworkflows lint` to work with new module structure for nf-test ([2494](https://github.com/nf-core/tools/pull/2494))
- Add option `--migrate-pytest` to create a subworkflow with nf-test taking into account an existing subworkflow ([2549](https://github.com/nf-core/tools/pull/2549))

General

- Update `schema build` functionality to automatically update defaults which have changed in the `nextflow.config`([2479](https://github.com/nf-core/tools/pull/2479))
- Change testing framework for modules and subworkflows from pytest to nf-test ([2490](https://github.com/nf-core/tools/pull/2490))
- `bump_version` keeps now the indentation level of the updated version entries ([2514](https://github.com/nf-core/tools/pull/2514))
- Add mypy to pre-commit config for the tools repo ([2545](https://github.com/nf-core/tools/pull/2545))
- Use Path objects for ComponentCreate and update the structure of components templates ([2551](https://github.com/nf-core/tools/pull/2551)).
- GitPod base image: swap tool installation back to `conda` from `mamba` ([2566](https://github.com/nf-core/tools/pull/2566)).
- Sort the `installed_by` list in `modules.json` ([2570](https://github.com/nf-core/tools/pull/2570)).
- Unset env variable JAVA_TOOL_OPTIONS in gitpod ([2569](https://github.com/nf-core/tools/pull/2569))

2.10

Template

- Fix links in `multiqc_config.yml` ([2372](https://github.com/nf-core/tools/pull/2372) and [#2412](https://github.com/nf-core/tools/pull/2412))
- Remove default false from nextflow_schema.json ([2376](https://github.com/nf-core/tools/pull/2376))
- Add module MULTIQC to modules.config ([2377](https://github.com/nf-core/tools/pull/2377))
- Add GitHub workflow for automated release announcements ([2382](https://github.com/nf-core/tools/pull/2382))
- Update the Code of Conduct ([2381](https://github.com/nf-core/tools/pull/2381))
- Save template information to `.nf-core.yml` and deprecate argument `--template-yaml` for `nf-core sync` ([2388](https://github.com/nf-core/tools/pull/2388) and [#2389](https://github.com/nf-core/tools/pull/2389))
- ([2397](https://github.com/nf-core/tools/pull/2397)) Remove fixed Ubuntu test and added to standard testing matrix
- ([2396](https://github.com/nf-core/tools/pull/2396)) Reduce container finding error to warning since the registries are not consistent.
- ([2415](https://github.com/nf-core/tools/pull/2415#issuecomment-1709847086)) Add autoMounts for apptainer.
- Remove `igenomes_base` from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
- Modified devcontainer permissions so that singularity can be run in Codespaces/VS Code devcontainers ([Commit a103f44](https://github.com/CarsonJM/tools/commit/a103f4484eca8c6d668e4653a4ed8d20faf1b41d))
- Update Gitpod profile resources to reflect base environment settings.
- ([747](https://github.com/nf-core/tools/issues/747)) Add to the template the code to dump the selected pipeline parameters into a json file.

Download

- Improved container image resolution and prioritization of http downloads over Docker URIs ([2364](https://github.com/nf-core/tools/pull/2364)).
- Registries provided with `-l`/`--container-library` will be ignored for modules with explicit container registry specifications ([2403](https://github.com/nf-core/tools/pull/2403)).
- Fix unintentional downloading of containers in test for the Tower download functionality. Bug reported by adamrtalbot and awgymer ([2434](https://github.com/nf-core/tools/pull/2434)).

Linting

- Add new command `nf-core subworkflows lint` ([2379](https://github.com/nf-core/tools/pull/2379))

Modules

Subworkflows

- Fix bug: missing subworkflow name when using `nf-core subworkflows create` ([2435](https://github.com/nf-core/tools/pull/2435))

General

- Initialise `docker_image_name` to fix `UnboundLocalError` error ([2374](https://github.com/nf-core/tools/pull/2374))
- Fix prompt pipeline revision during launch ([2375](https://github.com/nf-core/tools/pull/2375))
- Add a `create-params-file` command to create a YAML parameter file for a pipeline containing parameter documentation and defaults. ([2362](https://github.com/nf-core/tools/pull/2362))
- Update the Code of Conduct ([2381](https://github.com/nf-core/tools/pull/2381))
- Remove `--no-git` option from `nf-core create` ([2394](https://github.com/nf-core/tools/pull/2394))
- Throw warning when custom workflow name contains special characters ([2401](https://github.com/nf-core/tools/pull/2401))
- Bump version of nf-test snapshot files with `nf-core bump-version` ([2410](https://github.com/nf-core/tools/pull/2410))

2.9

Template

- `params.max_multiqc_email_size` is no longer required ([2273](https://github.com/nf-core/tools/pull/2273))
- Remove `cleanup = true` from `test_full.config` in pipeline template ([2279](https://github.com/nf-core/tools/pull/2279))
- Fix usage docs for specifying `params.yaml` ([2279](https://github.com/nf-core/tools/pull/2279))
- Added stub in modules template ([2277](https://github.com/nf-core/tools/pull/2277)) [Contributed by nvnieuwk]
- Move registry definitions out of profile scope ([2286])(https://github.com/nf-core/tools/pull/2286)
- Remove `aws_tower` profile ([2287])(https://github.com/nf-core/tools/pull/2287)
- Fixed the Slack report to include the pipeline name ([2291](https://github.com/nf-core/tools/pull/2291))
- Fix link in the MultiQC report to point to exact version of output docs ([2298](https://github.com/nf-core/tools/pull/2298))
- Updates seqeralabs/action-tower-launch to v2.0.0 ([2301](https://github.com/nf-core/tools/pull/2301))
- Remove schema validation from `lib` folder and use Nextflow [nf-validation plugin](https://nextflow-io.github.io/nf-validation/) instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
- Fix parsing of container directive when it is not typical nf-core format ([2306](https://github.com/nf-core/tools/pull/2306))
- Add ability to specify custom registry for linting modules, defaults to quay.io ([2313](https://github.com/nf-core/tools/pull/2313))
- Add `singularity.registry = 'quay.io'` in pipeline template ([2305](https://github.com/nf-core/tools/pull/2305))
- Add `apptainer.registry = 'quay.io'` in pipeline template ([2352](https://github.com/nf-core/tools/pull/2352))
- Bump minimum required NF version in pipeline template from `22.10.1` -> `23.04.0` ([2305](https://github.com/nf-core/tools/pull/2305))
- Add ability to interpret `docker.registry` from `nextflow.config` file. If not found defaults to quay.io. ([2318](https://github.com/nf-core/tools/pull/2318))
- Add functions to dynamically include pipeline tool citations in MultiQC methods description section for better reporting. ([2326](https://github.com/nf-core/tools/pull/2326))
- Remove `--tracedir` parameter ([2290](https://github.com/nf-core/tools/pull/2290))
- Incorrect config parameter warnings when customising pipeline template ([2333](https://github.com/nf-core/tools/pull/2333))
- Use markdown syntax in the description for the meta map channels ([2358](https://github.com/nf-core/tools/pull/2358))

Download

- Introduce a `--tower` flag for `nf-core download` to obtain pipelines in an offline format suited for [seqeralabs® Nextflow Tower](https://cloud.tower.nf/) ([#2247](https://github.com/nf-core/tools/pull/2247)).
- Refactored the CLI for `--singularity-cache` in `nf-core download` from a flag to an argument. The prior options were renamed to `amend` (container images are only saved in the `$NXF_SINGULARITY_CACHEDIR`) and `copy` (a copy of the image is saved with the download). `remote` was newly introduced and allows to provide a table of contents of a remote cache via an additional argument `--singularity-cache-index` ([2247](https://github.com/nf-core/tools/pull/2247)).
- Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter `--singularity-cache-index` introduced in [2247](https://github.com/nf-core/tools/pull/2247) has been renamed to `--container-cache-index` prior to release ([#2336](https://github.com/nf-core/tools/pull/2336)).
- To address issue [2311](https://github.com/nf-core/tools/issues/2311), a new parameter `--container-library` was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled ([#2336](https://github.com/nf-core/tools/pull/2336)).
- Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes [2346](https://github.com/nf-core/tools/pull/2346).
- Add apptainer to the list of false positive container strings ([2353](https://github.com/nf-core/tools/pull/2353)).

Updated CLI parameters

| Old parameter | New parameter |
| --------------------- | ---------------------------------------------- |
| new parameter | `-d` / `--download-configuration` |
| new parameter | `-t` / `--tower` |
| `-c`/ `--container` | `-s` / `--container-system <VALUE>` |
| new parameter | `-l` / `--container-library <VALUE>` |
| `--singularity-cache` | `-u` / `--container-cache-utilisation <VALUE>` |
| new parameter | `-i` / `--container-cache-index <VALUE>` |

_In addition, `-r` / `--revision` has been changed to a parameter that can be provided multiple times so several revisions can be downloaded at once._

Linting

- Warn if container access is denied ([2270](https://github.com/nf-core/tools/pull/2270))
- Error if module container specification has quay.io as prefix when it shouldn't have ([2278](https://github.com/nf-core/tools/pull/2278/files)
- Detect if container is 'simple name' and try to contact quay.io server by default ([2281](https://github.com/nf-core/tools/pull/2281))
- Warn about null/None/empty default values in `nextflow_schema.json` ([3328](https://github.com/nf-core/tools/pull/2328))
- Fix linting when creating a pipeline skipping some parts of the template and add CI test ([2330](https://github.com/nf-core/tools/pull/2330))

Modules

- Don't update `modules_json` object if a module is not updated ([2323](https://github.com/nf-core/tools/pull/2323))

Subworkflows

General

- GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency.
- GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config.
- Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([2312](https://github.com/nf-core/tools/pull/2312))
- Add CI tests to test running a pipeline when it's created from a template skipping different areas

2.8

Template

- Explicitly disable `conda` when a container profile ([2140](https://github.com/nf-core/tools/pull/2140))
- Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by jfy133]
- Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by jfy133, d4straub]
- Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([2170](https://github.com/nf-core/tools/pull/2170))
- Add a clean-up GHA which closes issues and PRs with specific labels ([2183](https://github.com/nf-core/tools/pull/2183))
- Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([https://github.com/nf-core/tools/pull/2194]) [Contributed by Midnighter, jfy133]
- Consistent syntax for branch checks in PRs ([2202](https://github.com/nf-core/tools/issues/2202))
- Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
- Updated AWS tests to use newly moved `seqeralabs/action-tower-launch` instead of `nf-core/tower-action`
- Remove `.cff` files from `.editorconfig` ([2145](https://github.com/nf-core/tools/pull/2145))
- Simplify pipeline README ([2186](https://github.com/nf-core/tools/issues/2186))
- Added support for the apptainer container engine via `-profile apptainer`. ([2244](https://github.com/nf-core/tools/issues/2244)) [Contributed by jfy133]
- Added config `docker.registry` to pipeline template for a configurable default container registry when using Docker containers. Defaults to `quay.io` ([2133](https://github.com/nf-core/tools/pull/2133))
- Add tower.yml file to the pipeline template ([2251](https://github.com/nf-core/tools/pull/2251))
- Add mastodon badge to README ([2253](https://github.com/nf-core/tools/pull/2253))
- Removed `quay.io` from all module Docker container references as this is now supplied at pipeline level. ([2249](https://github.com/nf-core/tools/pull/2249))
- Remove `CITATION.cff` file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline ([2059](https://github.com/nf-core/tools/pull/2059)).

Linting

- Update modules lint test to fail if enable_conda is found ([2213](https://github.com/nf-core/tools/pull/2213))
- Read module lint configuration from `.nf-core.yml`, not `.nf-core-lint.yml` ([2221](https://github.com/nf-core/tools/pull/2221))
- `nf-core schema lint` now defaults to linting `nextflow_schema.json` if no filename is provided ([2225](https://github.com/nf-core/tools/pull/2225))
- Warn if `/zenodo.XXXXXX` is present in the Readme ([2254](https://github.com/nf-core/tools/pull/2254))
- Lint all labels in a module ([2227](https://github.com/nf-core/tools/pull/2227))

Modules

- Add an `--empty-template` option to create a module without TODO statements or examples ([2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))
- Removed the `nf-core modules mulled` command and all its code dependencies ([2199](https://github.com/nf-core/tools/pull/2199)).
- Take into account the provided `--git_remote` URL when linting all modules ([2243](https://github.com/nf-core/tools/pull/2243)).

Subworkflows

- Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL ([2177](https://github.com/nf-core/tools/pull/2177))
- Fix `nf-core subworkflows test` not running subworkflow tests ([2181](https://github.com/nf-core/tools/pull/2181))
- Add tests for `nf-core subworkflows create-test-yml` ([2219](https://github.com/nf-core/tools/pull/2219))

General

- Deprecate Python 3.7 support because it reaches EOL ([2210](https://github.com/nf-core/tools/pull/2210))
- `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([2182](https://github.com/nf-core/tools/pull/2182)).
- Add a clean-up GHA which closes issues and PRs with specific labels ([2183](https://github.com/nf-core/tools/pull/2183))
- update minimum version of rich to 13.3.1 ([2185](https://github.com/nf-core/tools/pull/2185))
- Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([2196](https://github.com/nf-core/tools/pull/2196))
- Use `nfcore/gitpod:dev` container in the dev branch ([2196](https://github.com/nf-core/tools/pull/2196))
- Replace requests_mock with responses in test mocks ([2165](https://github.com/nf-core/tools/pull/2165)).
- Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([2228](https://github.com/nf-core/tools/pull/2228) [#2239](https://github.com/nf-core/tools/pull/2239)).
- Add the possibility to translate refgenie asset aliases to the ones used in a pipeline with an alias_translations.yaml file ([2242](https://github.com/nf-core/tools/pull/2242)).
- Add initial CHM13 support ([1988](https://github.com/nf-core/tools/issues/1988))

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